Here is a list of 12 proposed papers for our summer Journal club that focus on the general topic of Genomics. My definition of this term is rather broad so that we can include gene expression microarrays, proteomics, the new human genome databases, and SNPs. This is clearly a fast moving area, and I am perfectly willing to drop some of these papers in favor of recommendations from the class or some new blockbuster that turns up in the next few weeks.

By a consensus of opinion, I have chosen Wednesdays from 12 to 1:00 as our meeting time. We will meet in Coles 202 (Academic Computing) and proceed to a suitable classroom in Coles depending on how many people show up.

We have people signed up for all but 4 papers (2 per week). Look below and send me an e-mail if you wish to participate saying which paper you'd like to present.

Click on the titles to download the Journal articles in PDF format.

Week 1 (6/20): The basics of how microarrays work

Ferea TL, Brown PO. Observing the living genome.
Curr Opin Genet Dev. Dec 9(6):715-22, 1999.

Lipshutz RJ, Fodor SP, Gingeras TR, Lockhart DJ: High density synthetic oligonucleotide arrays.
Nat Genet 1999, 21:20-24.
[Affymetrix pats itself on the back.]

Week 2 (6/27): Basic bioinformatics of microarray data analysis

Scott Thomas
Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns.
Proc Natl Acad Sci USA 1998, 95:14863-14868.
[A hierarchical clustering method and data visualization tools for large-scale gene expression data sets are described.]

Kellam P. Microarray gene expression database: progress towards an international repository of gene expression data.
Genome Biology 2001 2(5): reports 4011.1-4011.3
[A short report on the status of public databases for microarray data]

Week 3 (7/11): Some pioneering studies

Week 4 (7/18): Some potential applications in diagnostics and drug development

Golub TR, Lander ES, et al.
Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring.
Science 258: 531-537, 1999.
[The proof-of-concept study for the use of microarrays to diagnose cancer types.]

Nichola Vjtovo
Marton MJ, DeRisi JL, Iyer VR Brown PO, et al.
Drug target validation and identification of secondary drug target effects using DNA microarrays
Nat Med 1998, 4:1293-301.
[The first data driven toxicogenomics paper]

Week 5 (7/25): Bioinformatics - finding transcription factors in co-regulated genes

Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM.
Systematic determination of genetic network architecture.
Nat Genet 22: 281-5, 1999.

Alon U, Barkai N, Notterman DA, Gish K, Ybarra S, Mack D, Levine AJ
Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays.
Proc Natl Acad Sci USA 1999, 96:6745-6750.
[This paper describes a clustering algorithm that can be used to classify genes on the basis of their expression patterns, and to group tumors and tissues according to their overall similarity in gene expression pattern. The method is applied to gene expression data from oligonucleotide array analysis of human colon tumors and normal colon tissue.]

Week 6 (8/1): Human SNPs & Pharmacogenomics

Debouck C, Goodfellow PN
DNA microarrays in drug discovery and development.
Nat Genet 1999, 21:48-50.

Week 7 (8/7): Human SNPs & Mouse vs. Human geome

Rada Norinskaya
The International SNP Map Working Group.
A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms.
Nature. 2001 Feb 15;409(6822):928-33.

+ two short commentaries in the same issue of Nature
Stoneking, M. Nature 409, 821–822 (2001).
Chakravarti, A. Nature 409, 822–823 (2001).

Dehal P, et al
Human Chromosome 19 and Related Regions in Mouse: Conservative and Lineage-Specifc Evolution.
Science 2001 293:104-111.

Alyssa's data